Summary quality control (QC) metrics
- Reporting tool version: 0.3
Coverage and number of variants
- Mean tumor coverage (fold): 63.02
- Mean normal coverage (fold): 32.8
- Total number of variants: 42157
- Total number of SNV: 40979
- Total number of small deletion: 989
- Total number of small insertion: 189
- Total number of structural variants (SV): 150
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| BND |
DEL |
DUP |
INS |
INV |
| 45 |
58 |
8 |
24 |
15 |
Purple purity and ploidy
- Estimated tumor purity (Purple): 0.99
- Estimated tumor ploidy (Purple): 3
- Inferred gender (Purple): MALE
- Whole-genome doubling (Purple): TRUE
Homologous recombination deficiency prediction (CHORD HRD)
- CHORD has not been tested extensively on long-reads dataset, so the prediction may not be accurate.
- In particular, we observed that CHORD can predict wrong results for samples with < 15X effective tumor coverage (effective tumor coverage = tumor coverage * tumor purity).
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| Sample |
Probability of BRCA1-type HRD |
Probability of BRCA2-type HRD |
Probability of HRD |
HRD status |
HRD type |
Remarks on HRD status |
Remarks on HRD type |
| COLO829_60-30 |
0 |
0 |
0 |
HR_proficient |
none |
NA |
NA |
Whole-genome copy number profile
- Copy number segmentation is done using CNVKit. The major and minor allele copy numbers are then estimated based on Purple’s estimated purity and ploidy.
- Note that purity and ploidy estimation can be unreliable at low coverage (<30X) and low tumor purity (<50%)
- This can subsequently affect allele-specific copy number estimation by CNVKit, although the segmentation should still be reasonable.
- For visualization purpose, if the major copy number is more than 5, the plot is capped at 5.
Small variants (SNV/INDEL) coverage and variant allele frequency (VAF) distribution
Mutational signatures
- Mutational signature is estimated using R package
MutationalPattern based on SNVs only (INDELs are ignored).
Table of filtered SNVs/INDELs
- Variants are filtered with any of the following criteria:
- IMPACT is HIGH
- Existing_variation contains COS (COSMIC variants)
- CLIN_SIG contains pathogenic
- CANCER_TYPE is not NA (variants that are in IntOGen Cancer Gene Census)
- CANCER_TYPE_ROLE and CANCER_TYPE_CGC_GENE are merged columns from CANCER_TYPE, ROLE and CGC_CANCER_GENE. These columns are collapsed into single entries separated by semicolon. E.g. CANCER_TYPE = “Breast;Prostate” and ROLE - “LoF;Act” means that the gene is a LoF in breast cancer and an Act in prostate cancer. This is done so that the table is more readable.
Table of filtered SVs
- SVs are filtered to only those that are part of the IntOGen Cancer Gene Census (CGC)
- Annotation based on AnnotSV. However to make the output readable some columns with very long information (e.g. “_coord” and “_source”) are removed. Please refer to original AnnotSV output for more information.
- Capital letter columns are from IntOGen CGC. Please see README from the IntOGen release for more information.
- CANCER_TYPE_ROLE and CANCER_TYPE_CGC_GENE are merged columns from CANCER_TYPE, ROLE and CGC_CANCER_GENE. These columns are collapsed into single entries separated by semicolon. E.g. CANCER_TYPE = “Breast;Prostate” and ROLE - “LoF;Act” means that the gene is a LoF in breast cancer and an Act in prostate cancer. This is done so that the table is more readable.
- Each SV can affect multiple genes. AnnotSV “splits” the different genes into different entries. This is why there are multiple rows with the same
AnnotSV_ID.
- ALT allele for insertion is hidden as “Too long” in the table. Please refer to the original AnnotSV output for more information.
- Note that Severus can call duplication as BND event, and AnnotSV has a tendency to annotate these as DEL event since it doesn’t make use of the “STRAND” information. Therefore, the “SV_type” column is not very accurate for BND events (You will recognize these with SEVERUS_BND in the ID column)
- The “SAMPLE” column represents the FORMAT column in the VCF. For Severus this is “GT:GQ:VAF:DR:DV”